Dependency analysis on package singleCellTK

General information

Bioconductor link link
Package version2.6.0
Number of strong dependencies369
Number of all dependencies398
Number of parent packages82
Max heaviness from parent packages33
Total heaviness from parent packages113
Number of parent packages (including Suggests and Enhances)99
Max co-heaviness from parent packages ("SoupX" and "Seurat")29

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of singleCellTK and columns are the dependency packages that each parent package brings in. On the right side of the heatmap, there are three barplot annotations: 1. number of imported functions/S4 methods/S4 classes from parent packages; 2. number of dependency packages from each parent package; 3. heaviness of each parent package on singleCellTK.

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats grDevices graphics tools grid stats4 splines parallel glue magrittr rlang Rcpp R6 crayon lattice Matrix pkgconfig lifecycle ellipsis digest jsonlite vctrs cli withr BiocGenerics pillar fansi utf8 tibble S4Vectors IRanges bitops fastmap Biobase mime matrixStats GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc MatrixGenerics cachem DelayedArray htmltools base64enc xtable GenomicRanges colorspace MASS SummarizedExperiment nlme rappdirs jquerylib RColorBrewer gtable codetools bslib sass fs mgcv scales farver labeling munsell viridisLite yaml later promises isoband commonmark ggplot2 curl httr openssl askpass sys BH png SingleCellExperiment httpuv fontawesome sourcetools stringi shiny stringr futile.logger snow lambda.r futile.options formatR BiocParallel sparseMatrixStats generics tidyselect purrr Biostrings htmlwidgets dplyr DelayedMatrixStats AnnotationDbi RSQLite DBI KEGGREST bit64 blob memoise plogr bit lazyeval beachmat irlba evaluate igraph plyr survival crosstalk highr xfun BiocSingular ScaledMatrix rsvd XML data.table knitr cluster gridExtra locfit gtools rprojroot BiocNeighbors RcppHNSW annotate scuttle edgeR limma dqrng sitmo RcppEigen gplots caTools KernSmooth rjson viridis cpp11 reshape2 Rtsne ggrepel BiocManager RcppArmadillo tidyr statmod abind AnnotationHub BiocFileCache BiocVersion interactiveDisplayBase dbplyr filelock DT assertthat xml2 rstudioapi callr processx ps GlobalOptions shape RcppTOML here tinytex gridGraphics graph HDF5Array rhdf5 rhdf5filters Rhdf5lib zoo patchwork bluster metapod miniUI prettyunits genefilter ggbeeswarm RcppML beeswarm vipor ExperimentHub rpart desc RcppAnnoy uwot RcppProgress FNN RSpectra R.oo R.methodsS3 circlize GetoptLong clue foreach doParallel iterators yulab.utils xgboost GSEABase numDeriv mvtnorm progress hms combinat scater scran rtracklayer Rsamtools BiocIO GenomicAlignments restfulr Rhtslib cowplot fitdistrplus future future.apply ggridges ica leiden lmtest pbapply plotly RANN reticulate ROCR scattermore sctransform SeuratObject spatstat.core spatstat.geom globals listenv parallelly progressr sp rgeos spatstat.data spatstat.random spatstat.utils spatstat.sparse tensor goftest deldir polyclip babelgene spam maps dotCall64 uuid ResidualMatrix pROC hgu95a.db org.Hs.eg.db R.utils Rdpack TFisher mutoss mathjaxr qqconf rbibutils sn plotrix multtest multcomp robustbase mnormt quantreg TH.data sandwich DEoptimR SparseM MatrixModels ape aplot ggfun tidytree treeio ggplotify shinyjs qvalue svMisc softImpute TrajectoryUtils fastICA mclust geneplotter ensembldb GenomicFeatures AnnotationFilter ProtGenerics biomaRt distr M3Drop pdist proxy ruv startupmsg sfsmisc bbmle reldist Hmisc bdsmatrix densEstBayes Formula latticeExtra nnet foreign htmlTable rstan rstantools RcppParallel StanHeaders jpeg checkmate inline loo pkgbuild backports enrichR MCMCprecision dbscan ComplexHeatmap multipanelfigure assertive.base assertive.files assertive.numbers assertive.properties assertive.types magick Seurat rmarkdown brio pkgload praise waldo diffobj rematch2 hunspell bookdown rex cyclocomp testthat xmlparsedata remotes rvest webshot svglite selectr systemfonts 0 2 4 6 8 Imported methods 0 50 100 150 Required packages 0 10 20 30 Heaviness from parents Biobase DelayedArray SummarizedExperiment SingleCellExperiment matrixStats methods tools yaml magrittr utils stats data.table KernSmooth rlang generics plyr tximport withr colorspace cluster Rtsne gridExtra limma R.utils S4Vectors Matrix circlize VAM igraph ROCR reshape2 ape BiocParallel multtest tibble reticulate DelayedMatrixStats dplyr DT msigdbr rmarkdown ComplexHeatmap TrajectoryUtils shiny shinyjs shinycssloaders ggplot2 cowplot ggrepel scuttle ggplotify fields shinyalert SingleR enrichR GSEABase batchelor scds GSVAdata DropletUtils metap ggtree scran colourpicker plotly fishpond MAST sva zinbwave GSVA scater ExperimentHub TSCAN DESeq2 celldex TENxPBMCData scDblFinder scRNAseq scMerge celda Seurat SoupX RColorBrewer fastmap BiocGenerics stringr Rsubread knitr spelling BiocStyle shinythemes shinyBS shinyWidgets testthat shinyjqui shinyFiles org.Mm.eg.db lintr kableExtra In total 369 packages are required directly or indirectly (398) when installing 'singleCellTK' (2.6.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'singleCellTK' Imported functions The whole namespace is imported Package is listed in 'Imports' but namespace is not imported


Dependency table

"Import" information is from the NAMESPACE file of singleCellTK.

imports: number of imported functions/objects; importMethods: number of imported S4 methods; importClasses: number of imported S4 classes.

Required packages: number of strong dependency packages for each of the parent package (or in other words, number of dependency packages the parent package brings in).

Heaviness from parent on singleCellTK: number of required packages that can be reduced if moving parent package to Suggests of singleCellTK.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on singleCellTK
Biobase Depends The whole set of functions/methods/classes from parent package is imported to the namespace of singleCellTK. 5 0
DelayedArray Depends The whole set of functions/methods/classes from parent package is imported to the namespace of singleCellTK. 14 0
SummarizedExperiment Depends 8 0 0 24 0
SingleCellExperiment Depends 4 0 0 25 0
scMerge Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 136 33
metap Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 56 18
celda Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 138 10
scRNAseq Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 124 7
ggtree Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 58 5
fields Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 43 4
GSVAdata Imports The whole set of functions/methods/classes from parent package is imported to the namespace of singleCellTK. 52 3
fishpond Imports The whole set of functions/methods/classes from parent package is imported to the namespace of singleCellTK. 66 3
TSCAN Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 86 3
msigdbr Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 22 2
rmarkdown Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 27 2
shinyalert Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 43 2
batchelor Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 50 2
scds Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 50 2
zinbwave Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 73 2
DESeq2 Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 93 2
tximport Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 3 1
VAM Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 9 1
shinycssloaders Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 35 1
SingleR Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 44 1
DropletUtils Imports The whole set of functions/methods/classes from parent package is imported to the namespace of singleCellTK. 52 1
colourpicker Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 63 1
MAST Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 67 1
sva Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 69 1
GSVA Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 79 1
celldex Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 97 1
TENxPBMCData Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 100 1
scDblFinder Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 110 1
SoupX Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 146 1
matrixStats Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 0 0
methods Imports 1 0 0 0 0
tools Imports 1 0 0 0 0
yaml Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 0 0
magrittr Imports 1 0 0 0 0
utils Imports 1 0 0 0 0
stats Imports 1 0 0 0 0
data.table Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 1 0
KernSmooth Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 1 0
rlang Imports 1 0 0 1 0
generics Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 1 0
plyr Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 3 0
withr Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 3 0
colorspace Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 4 0
cluster Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 4 0
Rtsne Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 4 0
gridExtra Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 5 0
limma Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 5 0
R.utils Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 5 0
S4Vectors Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 6 0
Matrix Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 7 0
circlize Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 9 0
igraph Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 10 0
ROCR Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 10 0
reshape2 Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 10 0
ape Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 11 0
BiocParallel Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 11 0
multtest Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 14 0
tibble Imports 1 0 0 15 0
reticulate Imports 3 0 0 16 0
DelayedMatrixStats Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 17 0
dplyr Imports 3 0 0 20 0
DT Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 20 0
ComplexHeatmap Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 28 0
TrajectoryUtils Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 29 0
shiny Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 34 0
shinyjs Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 35 0
ggplot2 Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 37 0
cowplot Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 38 0
ggrepel Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 39 0
scuttle Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 39 0
ggplotify Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 40 0
enrichR Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 47 0
GSEABase Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 49 0
scran Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 58 0
plotly Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 63 0
scater Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 85 0
ExperimentHub Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 86 0
Seurat Imports Parent package is listed in Imports of singleCellTK but no object from parent package is imported. 145 0
lintr Suggests No object is imported into the namespace of singleCellTK. 56 12
testthat Suggests No object is imported into the namespace of singleCellTK. 36 7
kableExtra Suggests No object is imported into the namespace of singleCellTK. 63 6
spelling Suggests No object is imported into the namespace of singleCellTK. 18 2
BiocStyle Suggests No object is imported into the namespace of singleCellTK. 30 2
Rsubread Suggests No object is imported into the namespace of singleCellTK. 8 1
shinythemes Suggests No object is imported into the namespace of singleCellTK. 35 1
shinyBS Suggests No object is imported into the namespace of singleCellTK. 35 1
shinyWidgets Suggests No object is imported into the namespace of singleCellTK. 35 1
shinyjqui Suggests No object is imported into the namespace of singleCellTK. 37 1
shinyFiles Suggests No object is imported into the namespace of singleCellTK. 42 1
org.Mm.eg.db Suggests No object is imported into the namespace of singleCellTK. 45 1
RColorBrewer Suggests No object is imported into the namespace of singleCellTK. 0 0
fastmap Suggests No object is imported into the namespace of singleCellTK. 0 0
BiocGenerics Suggests No object is imported into the namespace of singleCellTK. 4 0
stringr Suggests No object is imported into the namespace of singleCellTK. 7 0
knitr Suggests No object is imported into the namespace of singleCellTK. 12 0

The following table lists pairs of parent packages with co-heaviness larger than 10. The co-heaviness measures the number of additional dependencies that two parent packages simultaneously import and are only imported by the two parents.

Note the co-heaviness from parents can be always easily observed in the dependency heatmap.

Parent 1 Parent 2 Co-heaviness on singleCellTK Co-heaviness as Jaccard coeffcient
Seurat SoupX 29 0.967

Analysis was done with pkgndep.